Codemod db pass-through calls: messages + runs + approvals + company (C1 part 2/3)

Rewrite ~376 call sites for messages, runs, approvalsMod, and company
domains and delete the corresponding pass-through methods on
AppDatabase / AppDatabaseBase. Structural type references
(ReturnType<HandlerDeps["db"]["getRun"]>) and SweepStaleReviewsDeps-style
mocks are updated to route through the owning sub-module.

src/main/orchestration/initial-user-turn.ts

@@ -44,7 +44,7 @@ export function resolveInitialUserTurn(
   }
 
   if (trigger === "message" || trigger === "peer_request") {
-    const unread = deps.db.listAgentInboxUnread(companyId, agentId);
+    const unread = deps.db.messages.listAgentInboxUnread(companyId, agentId);
     if (unread.length > 0) {
       return buildCommunicationTurn(trigger, unread, deps.db);
     }